Mega Mewtwo Saga-Revised
by Kyokon-n
Summary: (Revised) This is a dark tale about a lost, misguided Mega Mewtwo Y who struggles with her emotions, and a violent, deranged Mega Mewtwo X who is set on destroying the human race. Each with their own companions, Giovanni's craving for the strongest pokemon starts with a risky and dangerous gamble, and ends with a war. Rated T for violence, theme, and occasional language.
1. Chapter 1

**Author's Note:** _Kyoko here! For some readers, you may recognize this story. But, while writing, I felt like the first time I started Mega Mewtwo Saga, it lacked something. So now, I'm rewriting it. With longer chapters, more in depth characters, and a new story line that hopefully will keep you wanting more!_

 _I hope you enjoy the new and improved Mega Mewtwo Saga!_

 _ **I do not own pokemon**_

 **January:**

I, Dr. Takumi Komata, has had the honor of being requested to join a project for Team Rocket, in which I will be the head scientist for the project. We have been given every piece of genetic material from the first artificial life, and have been ordered to create two new clones from the first failed experiment. To explain further, what I mean by "failed", I mean the clone was defiant, deadly, and currently roaming the region on it's own. This pokemon can only be described by incredibly dangerous. This Mewtwo is a strong psychic time, the clone of Mew. After its escape three years ago, it caused a tropical storm on New Island to lure pokemon trainers in an attempt to wipe out the entire human race.

This pokemon is indeed very powerful. It almost makes me wonder, is this wise? The first clone proved uncontrollable, and making two new, smarter clones is unwise at best. We have no guarantee they will obey, and no means to force it. The repercussions of such an experiment could be dangerous, even deadly, if they were to become even slightly agitated.

Project 002-25/26 will be done in what we estimate to be a year. The materials are being transported to the laboratory this week, and the scientists are getting settled in their dorms. Having these clones done within a year is an outrage, almost impossible - gestation for a human child is almost that long, and these clones will be much more advanced than a mere human infant. Maturity wise, the clones will be in what we would consider children, but with power and intelligence that would far surpass the original Mewtwo. We begin work next Monday, and each progress report will be updated at the end of every month.

We can predict very little of what we're about to create; we can only hope the world will not suffer with what we have done.

 **February:**

The clones have begun the gestation process! One of the scientists, Kimiko Karou, has willingly donated two of her pokemon to use their DNA in hopes to stabilize the clones. There was little genetic information left of Mewtwo, but combined with Kimiko's psychic pokemon and Ditto genomes, we have successfully started what could be the two greatest pokemon the world has ever seen! One clone will be Psychic/Fairy in type, stabilized with a young Ralts. The second clone will be Psychic/Fighting, stabilized with a Medicham.

This is an amazing scientific feat, creating two pokemon from almost nothing, who are not only skilled in one type, but two! We have had… acceptable losses, but nobody has focused on what was, only what will be!

We cannot determine what either clone will look like at this point. We can only assume they will both be bipedal, like the original clone and the pokemon they were derived from. The Psychic/Fighting clone will most likely have strong upper body strength. We cannot determine the gender of either. The original Mewtwo was depicted as genderless, and we have had a male and female pokemon donate their genes, but it is still entirely possible they can be genderless as the first Mewtwo. We assume in later months this important detail will be revealed!

For now, we are satisfied that they are growing. At this point, they are nothing more than a cluster of cells, but if they live to the next progress report, they will most likely live to full gestation. (In a side note, I do not expect the rest of the progress reports to be so lengthy, their growth will slow as they get older.)

 **March:**

The clones lived through March! They have grown at a steady rate, the speed is astounding! Currently they are about the size of an orange, and we are seeing the beginning of color and physical traits. We estimate the Psychic/Fighting type to be the bigger of the two, even now it is slightly larger. We assume they will be pale in pelt color, either white or a pale shade of purple. Each clone will have a tail, one being on the lower back and the other being on the base of one's skull.

We have labeled them "X" and "Y" for scientific purposes. "X" being the Psychic/Fighting and "Y" being the Psychic/Fairy.

The growth at this stage is essential. If anything is slightly off, it will ruin the entire experiment. Giovanni has sunk in thousands of dollars, and has made it clear failure is not an option.

 **April:**

Both clones have already grown significantly! Already the size of a human infant, in only two months! We have also possibly discovered the gender of the clones, "X" is male, being derived from a male Medicham. We assume "Y" is female for similar reasons.

Several scientists have suggested names for the clones, but I fear this may be a mistake. I try to keep them from doing such a thing, I see no good getting attached to them or forming a bond. Once they are "born", they will be tested and taught to fight… they will despise us by the end of this.

 **May:**

Giovanni himself came to inspect our progress a few days ago. It was apparent he was pleased with our work, and was even more excited when he learned of their genders. He raved about breeding, "an army of clones", he kept saying. I almost regret using the Ralts to stabilize "Y", it is most likely the reason she is female, and she could just be become an incubator for Giovanni's army of super pokemon.

As much as I wanted to avoid it, even I have gotten attached to these clones. Giovanni only refers to them as "it" and were he not my superior I would have corrected him. He sees them as nothing but tools of war.

 **June:**

Now the size of small children, their growth has slowed down. Their bodies have developed before their minds to prevent rapid brain growth with no room in the skull cavity to hold what will surely be a complex brain. But they continue to grow, and we believe they will open their eyes soon. They have both begun moving their limbs and tails slightly, and we expect that to improve within the next few months as well. These clones are truly a marvel. We plan on getting monitors to watch brain activity as they grow.

 **July:**

They anew remarkable, truly amazing! We have gotten brain activity monitors and hooked them up to the gestation tubes, and what we discovered is amazing! The clones are not only awake, but _aware._ Their brain activity is near constant, this shows that not only are their bodies developing, their minds are perfectly sound as well. They have grown so much in a small amount of time. They will just meet December's deadline, once they're awake fully, we can test their awareness to ensure Giovanni they are intelligent creatures.

…

 _A dull, throbbing pain enveloped it's mind. The pain never stopped, not fully, only lessened or intensified. The world around it buzzed, unaware of it's suffering._

…

 **August:**

Both clones have opened their eyes! "X" has deep sapphire eyes, while "Y" has red eyes. Despite being derived from the same pokemon, these two clones look almost nothing alike.

"X" has armor type plates over its hips, forearms, and shoulders. It has tri-fingered paw and toes. It's tail is upright. It is a pale Lavender color. But it's shoulder plates, underbelly, and tail are a deep purple.

"Y", on the other hand, is very small. It's fur is very pale, but the end of its "tail" attached to the base of its head is a slightly different purple. It's finger and toes are the same purple, and has a hood type appendage attached to its head.

They both started moving as well. "Y" is extremely curious, always watching our movements. Her face pressed against the glass of her growth tube has caused several laughing fits in the laboratory. "X" hasn't moved much, but we have noticed him holding his head quite a bit. We can't be sure what the cause is, we will have to wait until they are released to diagnose whatever problem there is.

 **September:**

We have decided to use a Gardevoir and a Medicham to train the clones when they are done maturing. We tested the clones reaction to their trainers, and we were quite surprised.

The Gardevoir seemed to form a bond with "Y". They both pressed their hands to the glass, and seemed to be communicating telepathically. The Gardevoir basement frantic once her trainer tried to recall her, and this only stressed out "Y". "Y" seemed to calm down once the Gardevoir left, but she kept her hands and face pressed against the glass until the lab staff left for the day.

"X", however, did not have such a sweet interaction with Medicham. They appeared to challenge one another, each took turns beating the glass with their palms. They each got progressively rougher, but without enough force to shatter the glass. This went on for a short while before the Medicham was satisfied, after which he left. I hope he will not be too tough on his pupil.

 **October:**

The clones are both at full size; their brains and internal organs are the only thing that needs to finish developing. "Y" is slightly smaller than the average adult woman, and is _odd_ to say the least. We have seen her hold the base of her tail several times, much like a human woman plays with her hair while she is nervous.

"X" is much larger, much larger than we ever expected. His gestation tube is smaller than he needs, but he is too far in development to change his habitat, the shock from the change in environment could be enough to stop his growth completely.

They are both great specimen. There is no flaw with either, they will make great fighters, just as Giovanni wanted.

 **November:**

There was a slight _issue_ at the beginning of the month. A scientist knocked an examination table into "Y's" gestation tank, and caused several cracks and water leakage. This caused a great deal of stress to "Y", she was not used to breathing air and we fear this might affect her development. But, as curious as "Y" is, she soon became accustomed to breathing air and started poking her head and limbs above the water.

Watching "Y" has become a laboratory pass time, we are astounded by her abundance of personality and awareness to her surroundings. "X" seems uninterested in the world, and spends the majority of the time with his eyes closed.

We plan on releasing both clones on December 30th.

 **December:**

The clones will be released in two days. I have to admit, I am very nervous. There is no way to predict how either pokemon will react, and there is very little we can do to control them if they react violently. We are not so concerned with "Y" even with her psychic abilities, she is smaller than most of the scientists working here, and childlike at best. "X", however, is the cause of most of our concern. He has cracked his gestation tube in several places this last month, and has started showing erratic, almost violent behavior.

We have taken precautions if one decides to cause problems, but If they become too aggressive I fear for our lives. They are, after all, animals - however intelligent they are. Giovanni has prepared a dorm room, much like us scientists live in, for the clones. Unlike ours, it will be filled with cameras to observe the clones behavior. We can never be too careful.

We have possibly created the two most powerful creatures in the world: The Mega Mewtwo.

 **Break**

 _Mew floated over the Team Rocket base, her long pink tail swishing slightly below her._

"Too late." _She thought to herself, feeling the clones presence in the laboratory below her. She rushed to Kanto when she heard of Giovanni's attempt to create another clone, but she was months too late. The rocky terrain surrounding the headquarters not only avoids any prying eyes, it made it extremely difficult for for the old legendary to find. She spent months searching Kanto, months she couldn't afford to waste, and now it was_ too late.

 _The weary Mew lowered herself to sit on the flat roof of the building, and concentrated all of her on the two pokemon in the laboratory located under the building. She gently psychically nudged one of the clones._

 _It proved to be a terrifying mistake._

…

 _An angry scream ripped through her mind send shattered reality. An image of the laboratory surfaced in her conscious, the lab covered in gore. Broken lights above flickered, giving a small mercy to the ones lying slain below. A clone levitated in the air over the destruction, the flickering lights gave almost a demonic edge to the clones evil grin._

 _It was a bloodbath, and the clone only laughed as it looked down at the countless murders it committed, but it's laughter was cut short. It clutched its head, growling and thrashing around in the air. It howled in pain, psychic energy spiked and lashed around the clone as it waged a war in its own mind…_

…

 _One clone held its palms out in front of it, a small ball of psychic energy crackling between its paws. Another pokemon, that Mew recognized to be the original Mewtwo, was besides the clone nodding with approval._

"Good, you have learned. This is the basis for every psychic attack, forming energy. When you have mastered this, we will work on more advanced attacks." _Mewtwo praised, earning an eager grin from the clone._

"This is easy!" _The clone bragged,_ "I'll have this down in no time!" _The clone launched the orb into the air, it's grin only widening as it's attack exploded into sparks in the air._

"Show off," _Mewtwo chuckled, walking into the set of caves Mew recognized to be Mewtwo's home in Mt. Quena. The clone turned around, and quickly vanished into the intricate system of caves with Mewtwo._

…

 _It screamed in terror. Nightmares plagued the clones mind, causing a relentless amount of anguish. Tossing and turning, the clone thrashed in it's sleep, tears welling up in its eyes as it]s subconscious unfolded a horrendous tale of slaughter, bloodshed, and rage. Blood of the murdered coated it's fur, but the smell only enticed it for more. Claws ripped into flesh, bu tthe clone found no satisfaction in dismembering the already dead. The3 screams of the sleeping were replaced with laughter in the dream, it's tear stained face was envisioned as a mask of blood. The clone grinned,_ this _is what living was._

 _Would this nightmare end up a reality?_

…

 _The clone's toes were dipped in one of many of Mt. Quena's pools of water. The clone giggled as a Goldeen swam up and gently nibbled on a toe. Blowing happy bubbles, the fish hopped out of the water and flapped it's fins. With both pokemon giggling and splashing around, it wasn't long until the clone was covered in water. Catching its breath, the clone watched the small fish swim in circles before a thought came to it's mind._

"Do fish like to be pet?" _It wondered, dipping a paw into the water. The Goldeen stopped spinning in the water to go nibble on the clones fingers, before allowing it to gently stroke the scales on it's underbelly. A small smile spread across its face as more fish swam up to the clone, the water soon becoming a flurry of bubbles._

"Maybe… Just maybe I'll stay." _It thought to itself, grinning at the school of fish._

…

 _Mew shuttered as she came back to reality, her mind reeling from the sudden psychic invasion._

"What just happened?" _Mew thought to herself,_ "Dreams… or visions?" _She began dissecting what she saw. Two visions of violence and suffering, two of peace._ "Have I seen their future? How will I guide each clone to their envisioned life?" _She thought for some time, how to avoid two visions and how to cause two._

 _Mew's tail continued to swish behind her as she calculated a plan. For now, she would stay here. She would not interfere unless she believed necessary, and would only observe from a safe distance, using the humans as her eyes. She would content herself with that, and bring the clones to Mewtwo when she had the chance._

 _But something deeply worried her. She felt the activity of the scientists, the sleeping clones, and the burden of an unmeasurable amount of sadness._


	2. Chapter 2

**I do not own pokemon!**

 _On December 30th, scientists scrambled around the laboratory, preparing to release the two clones. Half of the scientists began preparing what would be needed to examine the clones, the other half gathered what little materials they had to restrain the clones if need be. The head scientists, Dr. Takumi Komata, sat hunched over a computer, furiously typing what would be the last progress report for experiment 002-25/26. Next came more strenuous work, making sure each clone fulfilled their purpose._

 _Mew sat on a boulder outside the base, her eyes closed as she used a psychic link with one of the scientists so she could watch the clones "birth". She expected nothing but the worst, the glimpses of the future she saw several days ago haunted her as she held her breath, it was time to begin…_

 _ **Break**_

The room fell silent, but energy buzzed throughout the room as the entire scientist staff crowded around the gestation tubes. Dr. Komata broke through the crowd, and began fiddling with "Y"s tank, motioning for his colleague, Dr. Ushio, to do the same with "X's. After pressing the necessary buttons for making them drain, both men backed away from the tanks as they watched the water slowly seep out. Excited whispers broke out through the crowd, but the clones had a much different reaction to being brought into the world.

Both clones were shocked to have the water drained. "Y" sank to the bottom of the tank, then pressed her face against the glass to watch "X". "X" gasped for oxygenated water at first, but then stood to the best of his ability in the small tube after he got adjusted to air. Once the last of the water was sucked up, the glass was lowered, exposing both clones.

"Y" sat in the small tube, blinking in confusion as she scientists smiled down at their creations. "X" stood at full height, over seven feet tall, his sapphire eyes glaring at the people in the room. His agitation was evident, but the scientists paid no attention to his unnecessary anger.

"Welcome to the world, you two." Dr. Komata addressed the clones, "My name is Dr. Komata, and we are your creators." He said, grinning and motioning to the rest of the scientists.

" _Koh-Mah-Tah."_ A psychic voice was heard throughout the room, every scientist gasping as "Y's eyes widened at the response to her actions. The room was quiet as she levitated to Dr. Komata, pulling a pen out of his lab coat pocket and turning it over in her hands.

"My, she's as curious as we thought!" One scientist piped in, getting agreements in response.

"They are both a huge leap for pokemon science!" Another one quipped.

"Simply marvelous!" Dr. Ushio added.

"Let's begin the examinations." Dr. Komata decided, turning to his colleagues, "Prepare the examination supplies." He dictated, but was interrupted by a snap and a crowd of giggling scientists. He turned around, only to begin laughing himself.

"Y" had broken the pen, and had smeared blue ink all over her paws as she frantically tried to repair it. "X" only watched in annoyance before jumping off the tube base and onto the ground.

"Will you two come here?" Dr. Komata asked, his tone warm as he pointed to the two examination tables. "Y" levitated to one where Dr. Ushio motioned for her to sit. She tucked her tail behind her as she gracefully sat, and watched along with everyone else as "X" made no move to do what they were told. "X" only stared back at his creators until Dr. Komata grew impatient.

"Your cooperation is appreciated." Dr. Komata said to "X", a hint of warning in his voice. "X" growled slightly, but stomped to the table and sat down, crossing his arms and glaring. "Very nice," Dr. Komata praised, then handed Dr. Ushio a flashlight. He pulled another for himself out of his coat pocket, "Dr. Karou, will you finish preparing the needles to extract a blood sample when we're done testing their light reaction?" Dr. Kaoru nodded and left the lab as Dr. Ushio turned to "Y".

"This won't hurt, but it's very bright," he explained, waving the flashlight. "Y" ignored the flashlight and reached out to lightly tug on his beard. "Now, now," He said, chuckling as moved her paw and grasped her cheek, "Try to keep your eye open." He instructed, shining the light into her red eyes. "Y" squeaked and pulled her head back, looking at the doctor with a hurt expression as she grasped her tail in her paws. "See, you're okay." He said gently, patting her on the head.

"What a good girl!" A scientist commented, writing her reaction down on a laptop. "Okay, I'm done, time for "X", the scientist announced, and all eyes turned to "X".

"Just be still." Dr. Komata ordered, pointing the light at "X". "Ready?" He asked, but "X" only got a slight growl in response.

Once the flashlight was turned on, "X"s mind became a blinding pain. With a roar, "X"s tail lashed out behind him, hitting Dr. Ushio in the stomach, a sharp crack indicating broken ribs. Growling in a mixture of pain and rage, "X" brought a fist down on the examination table, cracking it in two. "Y" watched in horror as four scientists rushed to restrain "X", only to be thrown back away from the angry pokemon.

 _Mew panicked as she watched what was happening through a psychic link._ "I have to stop him," _She thought, hyperventilating until she found a solution._

 _She charged all of her psychic energy, only to bombard "X" with all of it at once. Losing her energy, Mew disconnected the psychic link, hoping what she did was enough as she fell over with fatigue…_

"X" staggered, his hazy mind became numb and suddenly he couldn't hold himself up. He slumped to the floor, and the scientists that weren't injured took the opportunity to use the restraints prepared. Dr. Ushio was taken to get his broken ribs set by two scientists, and "X" was quickly strapped to the remaining examination table without a fight. He struggled to stay conscious, but growled when a nervous "Y" levitated over to him.

" _Be calm!"_ She pleaded, " _Fighting will do you no good!"_ She explained nervously, but got no answer from the other clone. He did not stop growling, and instead wiggled in his restraints.

"It seems "Y" is using telepathy to communicate with "X"! I can guarantee she has been listening to us!" Dr. Komata gushed as he looked to "Y", smiling at her small nod in agreement.

"We have names for you two. "X" and "Y" don't seem all that appropriate now, Instead, we have taken the "X" and "Y' from the greek alphabet, Chi and Upsilon." Upsilon grinned at her name, while Chi only closed his eyes warily. It was clear his outburst and Mew's unknown psychic attack had taken a toll on him.

"Would you like to see your dorm, Upsilon?" Dr. Komata asked, smiling as Upsilon's eyes lit up in an eager agreement. "Chi will be joining you… later." Dr. Komata added, looking over at the dazed clone who was held hostage on the examination table.

"Then let's go." He smiled, motioning for her to follow him out of the door.

 **Break**

The dorm was along the same hallway as the laboratory, away from the scientists quarters but close enough that the clones could be watched. Dr. Komata and Upsilon traveled in silence, Upsilon levitated a few feet behind her creator, not fully aware of where she was going or who she was following. She was fully entranced by the pen ink, she floated with her hands in front of her face until she bumped into Dr. Komata's back.

"This is where you will stay," He explained as he unlocked the door, "It's small but I'm sure you will not need an abundance of space anyway." He gently took a dirty paw and her inside, "Here, let's clean you up." He chuckled, dragging her to the kitchen sink. Dr. Komata pushed a small button near the faucet, and a small stream of warm water poured out.

Upsilon only watched as Dr. Komata ran the water over her paws. "We'll have our hands full with you, won't we?" He laughed, scrubbing her fur clean.

" _Then do not hold me."_ She replied, cocking her head. Once she was clean, she wiggled her wet fingers, mesmerized by the sensation.

"It's a figure of speech," He informed her while walking to a large white cushion, "This is your bed," he said. He unfolded a large white blanket and spread it over the cushion as Upsilon levitated over to it. "Use this when you are cold." He said, smoothing out the blanket. Upsilon ran her tail over the fuzzy blanket before gasping and leaping face first on the cushion, purring with satisfaction from the warm blanket.

" _It's so soft!"_ She purred, rolling and wrapping the blanket around her.

"I'm glad you like it." Dr. Komata said, laughing at her behavior. "Now, Chi's bed is on the other side of the room, I trust you will inform him when his behavior is well enough to come." He said, and Upsilon nodded in response.

"Now, I have some more tests to do on Chi. Someone will probably be back to get you tomorrow," Dr. Komata said as he walked out of the dorm. "Be good, Upsilon." He said with a smile, shutting the door.

As the door closed, she sat up on her cushion. She was all alone, and she didn't like it.

 **Break**

 _Takumi Komata briskly walked down the hallway, trying to not only control his breathing, but also his anger. "Chi is_ already _proved to be a problem," he thought to himself as he smiled as a colleague. "I did not work an entire year for_ this." _He thought angrily, storming into the laboratory. Dr. Ushio, his ribs now set, and Dr. Kaoru sat around a small table drinking coffee. Both looked up when he walked in, and both looked how he felt._

" _What can we do?" Dr. Ushio asked quietly._

" _He will behave or we will make him." Dr. Komata decided, and he sat at the table with them._

" _Here," Dr. Kaoru pushed her coffee mug to him. "I've had enough, you can finish it."_

" _Thank you," He responded, and brought the mug to his lips, but set it back down before taking a sip. "I have an idea." He said suddenly, looking over at the clone. "Let's try to finish it tonight. We have a schedule to keep." He said, and began explaining his plan._

 _It would take them the entire night to finish._


	3. Chapter 3

**I do not own pokemon!**

Upsilon was woken up at seven am by Dr. Ushio, who told her they would begin training today. Upsilon, who was hesitant to get up off the soft cushion, but after some persistence, sleepily followed him through the hallway. She hovered beside him, and asked questions the entire way to the arena.

" _Where are we going?"_ She asked.

"At the end of this hallway there is a training arena. We will be going there." He said shortly.

" _What are we training for?"_

"So you will be strong."

" _Will Chi be there?"_

"Yes."

She got close to her face, her muzzle close to the touching his cheek. " _What are those hairs on your face?"_

"It's a beard." She reached out and stroked his chin.

" _Can I grow one?"_ She asked, putting her hand away.

He laughed, "You are female."

" _Is that a no?"_ She pouted.

"Yes, Upsilon."

" _Yes to no, or yes to a beard?"_

This continued until they got to a wide set of double doors, indicating they were at the training arena. Dr. Ushio opened the doors, but did not follow Upsilon inside. "Your instructors are inside. Someone will come get you once you are done." He explained, closing the doors once her was finished talking.

She floated into the arena. Chi, a Gardevoir, and another pokemon she had never seen was already there, and they were all waiting for her. Chi leaned against the far wall, an angry look in his eye. He had two metal bands around his wrists, each one glowing slightly. The pokemon she hadn't seen before was levitating beside him, it's eyes closed. The Gardevoir said something to the unknown pokemon before rushing to meet her in the middle of the arena.

" _Hello!"_ Upsilon said excitedly, levitating to be the same height as the Gardevoir.

" _My, how you've grown since I saw you last!"_ She replied, grinning at Upsilon. " _I will be training you to be strong,"_ She explained, " _as strong as you can be."_

Upsilon began to answer, but Chi was thrown across the arena and landed with a thud by the

doorway. But Upsilon and her trainer turned to look at the foreign pokemon in shock.

" _Moe!"_ The Gardevoir gasped, but was ignored as Moe strode towards Chi.

" _He will not learn from a soft teacher."_ He angrily started, grabbing Chi by the tail and hurling him up into the air. " _Showing the full strength of an opponent will make a pupil learn to defend themselves, and be just as skilled on the offense as well."_ His foot connected with Chi's stomach, " _Not because he wants too, but because_ he must." With a final jab, Chi fell into a crumpled heap on the ground, no longer attempting to fight back.

" _STOP!"_ Upsilon screeched, flying to come in between Moe and Chi. Moe's fist lost it's psychic glow as it fell to his side, and he glared at Upsilon. The Gardevoir ran to Upsilon, and pulled her away.

" _Moe is dangerous. Do not oppose him."_ She said, fear in her eyes as she pulled the clone to the other side of the stadium. Upsilon let herself be separated from the other clone, but watched as he struggled to get up. Moe loomed over Chi, lecturing him about his Psychic abilities.

" _It will allow you to do many things,"_ He lectured, " _But if you do not learn how to control it, and your anger, it will be your downfall."_

He only got a small growl in response.

 **Break**

Upsilon's lessons were much more civil. The Gardevoir, who she later found out was named Michiko, had a much more gentle method of teaching. They began with channeling Upsilon's psychic energy through her hands, then moved on to making small psychic sparks. They took short, frequent breaks and alternated between tasks until Upsilon could gather enough energy to make a small fuzzy orb of white energy.

When Michiko decided Upsilon had done enough for the day, they both sat on the ground for Michiko to demonstrate meditation. Michiko pleaded for Upsilon not to look at Chi, but she couldn't resist a few glances.

Still lecturing, Moe punched and kicked Chi throughout talking. Chi laid on the ground, his eyes closed, and Upsilon wondered if he was even conscious. He simply allowed Moe to abuse him without so much as wincing in return.

" _I do not approve of his way of teaching,"_ Michiko said sadly, moving Upsilon's gaze toward her instead. " _Yes, Chi will learn, and yes, he will be strong. But he is learning for the wrong reasons,"_ She shook her head, " _His heart along with his sanity will soon shatter if this continues."_

" _Why are you teaching us? What is the reason Chi must go through that torture?"_ Upsilon asked, appalled the nice scientists would let this happen.

" _You are the greatest pokemon ever born or created. We are here to guide you to your full potential."_ Michiko explained.

" _Well then what are you?"_ Upsilon asked.

" _I am a Gardevoir,"_ Michiko giggled, lifting her arms in a playful manner to show herself off.

" _Am I a Gardevoir?"_ Upsilon continued, looking down at her paws. She didn't _look_ like a Gardevoir.

" _You were created from my evolution line, but we are not the same."_ She paused, " _You are a Mega Mewtwo."_ She mused for a moment, her laughter gone as she bit her bottom lip. Upsilon knew she upset Michiko, and was going to change the subject, but Michiko broke the silence with a fake grin. " _So! Tell me about your time here so far?"_ She folded her legs and smiled warmly at the clone, waiting for an answer.

" _A light was shined in my eyes, and Chi was forced onto a table,"_ Upsilon thought out loud, " _Then I saw my room and slept on something really soft and then the man with the beard brought me here."_ She rambled, before shrugging and holding her tail, " _That's it."_

" _Very eventful for only a day and a half!"_ Michiko gushed. " _I will do what I can to make your time here as easy as possible,"_ She added, smiling down at the clone.

Michiko and Upsilon talked for the rest of the training session, and Upsilon was asked to practice meditation on her own to get a better control of her psychic energy. It wasn't long after she agreed to this that Dr. Komata and Dr. Kaoru came into the arena to collect the clones. Michiko and Upsilon got up easily and levitated to the two scientists, but Chi had a much more difficult time getting up. His entire body was bloody and bruised, and he struggled to get up off the ground. Moe glared down at him, and only watched Chi as he eventually got himself on his feet. But once he did, Moe leaped into the air and kicked Chi in the back, sending him flying towards the entrance of the arena.

" _I fully expect you to get better by the time we train next."_ He said coldly, and strode to stand beside his trainer. Michiko said nothing, but was radiating waves of sympathy and privately argued with Moe until Dr. Karou returned them both to their pokeballs. Upsilon flew to Chi, and tried to help him up, but Chi violently lashed out at her and avoided her assistance.

" _I do not need your help!"_ He howled, staring at her coldly with his sapphire eyes. He had managed to his knees, but didn't have the strength to stand fully. He fell into a heap on the ground, and Upsilon flew around him frantically until Dr. Komata pulled out his cell phone. He talked to the person on the other end and Dr. Kaoru for a few minutes before they came to the conclusion it would be better to bring a stretcher for Chi.

After putting his cell phone away, Dr. Komata motioned for Upsilon to come with him, "You'll see Chi later, let's go for now." He decided, and opened the door for Upsilon to leave, but she looked back at Chi several times before finally leaving.

 **Break**

After walking around for a bit with Dr. Komata, Upsilon realized the entire floor looked the same. White walls, white tile floors, with no unnecessary decorations or items. Dr. Komata explained there were several other floors, and that she was free to roam around the basement floor as long as she didn't touch anything. Upsilon was quiet for the most part, but after a while of following Dr. Komata around she got bored. She had almost decided she had had enough when Dr. Komata's phone rang, and once he was done talking asked if Upsilon would like to go see Chi. She eagerly agreed, Chi had been in the back of her mind since she left the arena.

They were close to the main lab, so it didn't take long for them to get there. Once Upsilon saw the doorway to the lab, she flew past Dr. Komata and right to the table Chi was resting on. He was bandaged up and there were several parts of his body that had been stitched up, but he looked unconscious.

" _Chi…"_ Upsilon whispered sadly, but her attention shifted once a large hand was placed on her back.

She whirled around. A tall man in a burnt orange suit had his hand outstretched towards her, with a smile that was a little _too_ nice. He smelled of alcohol, and the way he was staring at her made Upsilon uncomfortable. She didn't trust him.

"You are Y?" The man asked. He smiled wider, his tone was friendly but it only made her warier.

" _Upsilon,"_ She corrected him.

He looked stunned, "What?" He asked, looking at her incredulously.

" _My name is Upsilon. Who are you?"_ She asked, her tone rude.

"Upsilon, this is Giovanni." Dr. Ushio cut in, "He's the one who paid and hired us for your creation," He explained.

"I am your owner." Giovanni finished for Dr. Ushio, shooting Upsilon another smile.

" _Your voice is friendly, but your eyes are cold."_ Upsilon noted, getting shocked looks from both the scientist and her 'owner'.

" _Upsilon!"_ Dr. Ushio gasped, but Giovanni waved his embarrassment off.

"My dear, I am the reason you exist. I am the leader of this organization. You simply do not know me, that's why you are wary of me, and that is smart of you." He praised, but his voice was cold. "Do not be afraid, anything you want I will give to you." He smiled again, "Possessions, fame, _a mate,"_ He suggested, motioning to the unconscious Chi behind her.

" _I would like to leave."_ She said sharply, turning to fly out of the door, but Giovanni grabbed her tail and yanked her back.

"It is in your best interest to mind me, clone." He advised in a low tone, but let her tail go after he finished talking. She darted out of the room, cringing at the feeling of his breath on the side of her face.

" _Forgive me, Chi,"_ Upsilon thought as she flew down the hallway to her dorm, " _I cannot be in the presence of that terrifying man!"_

 **Break**

Dr. Ushio, Dr. Kaoru, and Dr. Komata stood in the laboratory with Giovanni, who was currently sitting on one of the plastic chairs scattered in the room, staring down the the three of them.

"It hasn't even been a week," Giovanni started, "And one is a failure, and one is defiant." He stood up and briskly walked to the door. "If they become a problem, solve it. The male already had psychic restraints. Do what you must with the female to ensure success, or don't waste time on Project 002-25/26 any longer." He demanded icily, then left the room.

 **Break**

 _Mew had gathered the strength to teleport herself to Mt. Quena, Mewtwo's home. The two of them sat in the moonlight, and shared a meal of the bountiful fruit that grew in Mt. Quena as Mew filled her clone in on the details of what had happened._

"I fear you cannot handle this on your own, Mew." _Mewtwo confessed, gazing at the legendary with concern. She was old, very old, but she hadn't shown her age until the past few months. She had seen a prophecy of the clones, but it was vague and only caused panic, not insight. Mewtwo had agreed to assist in any way he could, and was willing to take in the clones once they had been liberated from Team Rocket._

"I will be fine," _She reassured him, but he wasn't convinced. They talked strategy, trying to concoct a plan to get the clones in their custody. Mew_ wanted _them to escape, but not only for their sake, but for Mewtwo's as well._ "They do not know the danger they are in," _She thought,_ "If Mewtwo sees he is not the only one of his species, he may open his heart."

 _They finally thought of a plan. It was risky, but it might work._

"There is only one hope for us," _Mew said wearily,_ "We have one chance to free these clones, but following through will be tricky…"


	4. Chapter 4

**I do not own pokemon!**

 **Warning:** There is a bit of violence in this chapter, it's nothing too explicit, but I thought I should just give everyone a heads up.

The next day, Dr. Kaoru was the one to wake Upsilon up. She was less friendly than the other two scientists Upsilon knew, but wasn't uncomfortable to be around in any way. She led Upsilon back to the arena she and Chi trained in the day before, but Upsilon noticed Chi was nowhere to be found, and Dr. Komata was waiting in the arena for her. Two pokemon she had never seen before were standing on opposite sides of him, one was a large elephant with long tusks and a stern glare, and the other was a gray and black wolf.

"He is still weak from yesterday, he isn't in the top condition we need him to be for this particular training." Dr. Kaoru explained once Upsilon questioned her. "You'll see him soon," She said gently, seeing her expression, "We're just fixing him up," She reassured her, and then released Michiko before saying her goodbyes.

Michiko seemed anxious, and darted her gaze in between Upsilon and the other pokemon. " _You are to fight these pokemon, Etsu."_ She told her through telepathy, " _One is a ground type, a Donphan. The other is your weakness, a Dark Type named Mightyena."_ She explained, but paused when she saw Upsilon's anxiety. " _Your first battle with the Donphan will determine if you fight Mightyena today."_ She smiled, " _Do not worry, I will help you. You can do this, Dear Etsu."_ She finished, then turned to the side lines and nodded to Dr. Komata.

"Just do your best, Upsilon," Dr. Komata encouraged her, "Ready? Donphan, go!" He commanded. With the order, Donphan rolled into a ball and launched itself at Upsilon, who only stared in shock.

" _This is an attack called Rollout,"_ Michiko explained, " _Remember the psychic sparks I showed you how to make yesterday? Make one and shoot it towards Donphan,"_ She advised. Upsilon gathered the energy, but began to panic as Donphan approached at a much faster pace. She clenched her eyes shut, and stuck a paw out to shoot the sparks, and only opened her eyes when she heard the Donphan cry out in pain. Her eyes jerked open, and saw the Donphan stunned and stopped dead in it's tracks.

" _Good!"_ Michiko cheered, " _Now, fly up and then land hard on the Donphan's back. We will call this_ _Body Slam,"_ She ended. It seemed inhumane for Upsilon to attack the pokemon who still hadn't recovered from the last move, but she put her trust in her trainer and followed Michiko's directions regardless. She flew to around the center of the room, and slammed down on Donphan's back. Her opponent groaned heavily then slumped onto the floor, and Upsilon began to panic.

" _I killed it!"_ She screamed, looking down at what she did. She flew as high and far away from the pokemon laying on the ground as she could, then whipped around and glared at Michiko with all the hatred she could muster. Michiko simply stared back with a slight smile, and her reaction only angered Upsilon more. " _You made me do this!"_ She shrieked, pointing at Michiko, " _How could you? I_ trusted _you!"_ She raged, and was close to the point of tears. Michiko said nothing, and simply walked over to the Donphan and put her hand on it's snout.

" _Etsu, look. He is not dead,"_ She said calmly, bringing her attention to the Donphan, who was slowly getting up and shaking off the damage she did. Mr. Komata walked over to Donphan and pulled out a few spray bottles, and began spraying the ground type pokemon as Upsilon flew back over to inspect her opponent. She circled the pokemon she thought she had killed, then ran a paw over the pokemon to make sure what she saw was real.

" _I thought I killed you!"_ She yelped, causing the Donphan to chuckle in response.

"Donphan phan phan don, phan donphan." " _I'm more sturdy than that, but your concern is appreciated."_ He said, still chuckling.

" _Do not worry, Upsilon. Pokemon are harder to kill than that, and if you kill one, you will most definitely know."_ Michiko said, trying to comfort the still shaking clone. But she finally sighed in relief, his death would have weighed on her.

Dr. Komata broke in, clapping. "Very nice," He smiled, "You did excellent. But, I think that's all the battling we will do today. Michiko's trainer had informed me that you mostly just know Psychic Type moves, and that will not do anything to this Dark Type pokemon," He motioned to the Mightyena standing beside him. "We will try again when you know a wider variety of moves." He decided, then nodded once. "Michiko, will you focus today on mostly physical moves instead of special?" He asked her.

" _That is no problem, Professor."_ She replied. Dr. Komata thanked her, and praised Upsilon one more time before leaving with the Mightyena and the Donphan. " _Well,"_ Michiko began, " _Let us begin."_

They did as Dr. Komata asked, and focused on the physical side of training, and not the special. First, Michiko placed weak orbs of energy throughout the room, and Upsilon's task was to use a body slam attack on whichever orb she lit up. After Upsilon had disintegrated every orb of energy, Michiko taught her to shoot a star attack from her palms, much like the sparks of energy she could form. Then, they focused the rest of the training session on a powerful psychic attack.

" _This is a strong attack, and it will take you a while to master it,"_ She began, " _You will need to learn how to control your psychic energy, and Psyshock will become a devastating move."_ She demonstrated what she meant, closing her eyes and throwing up her arms with flourish as large psychic shock waves warped the space around the two. It rippled and shook with the force of the energy, and with a exclamation for Upsilon to watch out, she released all the energy, sending it several feet around her.

" _Can I do that?"_ Upsilon asked in awe.

" _That's our goal, we shall see."_ Michiko replied with a giggle.

 **Break**

They practiced for hours, and while Upsilon's attack was nowhere near as powerful as Michiko's, it was still an improvement. They decided to take a break, and end the training session with more meditation. They sat cross legged, but Upsilon could only float a few inches off the ground. Michiko, however, was several feet off the ground as she explained what to do.

" _Simply focus on the energy flowing through you. You will begin to notice it, and with the more energy you can gather, the more powerful your attacks can be, and the higher you can levitate."_

" _How high am I so far?"_ Upsilon asked curiously.

Michiko chuckled, " _It is not about how high you start, but how high you finish. You cannot focus on the present, work towards the future."_ She lectured lightly, but did open her eyes to observe her pupil's progress. But once she opened her eyes, she gasped and lost her focus, and tumbled to the ground.

A shimmery image of a Mew was projected in front of her, and watched her fall without a change in its facial expression. It floated down to look her in the eye before evaporating completely, leaving her shaken and confused. She stood up and brushed herself on, then got Upsilon's attention. " _You have done well, but I think it's best if we end today's lesson."_ She tried to hide the fear and confusion in her voice, but Upsilon wasn't fooled.

She didn't stop levitating, but opened her red eyes and straightened her posture. " _Is everything okay?"_ She asked.

" _Yes, Etsu. I am just a bit fatigued, that is all."_ She smiled, and Upsilon didn't question her further. " _Let's go to the lab. Dr. Komata will be impressed with your progress."_ She promised, and that seemed to cheer up the clone. They swiftly left the arena, but didn't talk much as Michiko led them down the hallway. She was deep in thought, the recent events of the past month replaying in her mind.

" _I have felt the strange presence of a psychic pokemon for some time now… I have never seen it, or spoken with it, but that_ has _to be it."_ She thought, the unseen force causing her a great deal of worry.

 **Break**

While Upsilon had spent the day training, Chi had spent it in the lab. His entire body ached from the previous day, and it left him little strength to fight against the scientists. Throughout the day, he had heard many praises to Upsilon, and this had caused him to feel a great deal of resentment towards the smaller clone. From what he picked up from their conversations, Upsilon was excelling, she had won her first battle and was picking up on human speech and mannerisms. _He_ on the other hand, was a dumb animal who had to be packed with steroids and injected with tranquilizers just to make him worth the money used to make him.

" _She was given a kind trainer,"_ He thought to himself. He was strapped to a lab bench that was stood up vertically, but he had enough movement to turn his head and glare at Moe, who was standing next to his trainer, smirking evilly at him. " _Mine beat him into an oblivion."_ He kept eye contact with Moe until a scientist stuck him with a needle, after which he hissed and jerked away violently. This injection _stung_ , it burned as it flowed through his veins and he felt his hazy headache return. He growled as the pain heightened, every needle that was stuck in the various parts of his body brought the pain to a new level until he was close to seeing red.

" _I bet_ Upsilon _could handle that pain."_ Moe taunted as he watched Chi growl and grimace in pain.

That comment is what broke him.

Chi fell into an uncontrollable rage. Psychic energy erupted around him, denting the table he was strapped too and disintegrating the leather straps. Swinging his fists in rage, he flailed around until his fist impacted with something, and a scream of pain indicated it was one of the female scientists. He caused chaos in the lab he was conceived in, using all of the psychic energy he could muster, he sent a shockwave of power throughout the room, shattering glass and injuring everyone in the room. His vision was hazy, but he could still make out the room, and his goal was to _kill_ , or at the very least make sure no one left without an injury. Lifting a young man without a lab coat up, he slammed him down on the broken gestation tube, impaling him before turning his attention to someone else, leaving him bleeding and screaming.

 _Why was she better? why was she treated as if she was more intelligent, more sentient, into a savage_ animal _like he was? Why was she given the kind trainer, while his beat him senseless, past the point of exhaustion and what was considered humane, just for a sick excuse of a lesson?_

…

 _After a Mach Punch in the stomach, Chi couldn't bear anymore, and tumbled to the ground, struggling to breathe and spitting the pooling blood out of his mouth._

 _Moe loomed over him, and kicked him in the face._ "You're supposed to be the best pokemon there ever was. You're supposed to rival even Mew. You're just a pathetic genetic experiment, you're a _waste of my time_." _He stopped beating him to turn and look towards the other clone._ "You should be doing well, like her. But you're just lying on the floor, you're completely useless." _He sneered, and jerked him up by the arm. He slung him up into the air, and then sent a flurry of kicks and punches directly to Chi's face, chest and stomach. He let him fall back onto the ground, and blood began to pool on the floor. Chi managed to lift himself up, and looked over to Upsilon and her trainer._

 _And what he saw enraged him to the point of no return._

 _They both had their backs turned to him, Upsilon was floating and Michiko was standing on the ground. They were both giggling about something unknown to him, and they began laughing so hard Upsilon tumbled out of the air and onto the ground. Michiko pulled her off the ground, smiling fondly as she brushed the dirt off Upsilon._

"Now, watch me, Etsu," _She said, and then cupped her hands. She closed her eyes, and psychic energy brimmed and overflowed from her palms. It cascaded in waves down to her feet, and Upsilon gazed in awe as she stuck the base of her tail into the river of energy._ "Like that, focus your energy to your palms. You will only be able to make sparks today, but you will get better with practice." _Upsilon smiled up at her, and Michiko returned her gaze with the same amount of love._

"Michiko?" _Upsilon broke the silence suddenly._

"What is it, My Dear?" _She asked._

"What does Etsu mean? _She cocked her head to the side._

 _She grinned as she replied,_ "It means 'Delight', little one."

"Am I a delight?"

"You have given me a joy I was sure I had lost forever, and for that you are very special to me." _She replied, smiling and pulling her into a hug._

 _Their conversation was stopped short when Upsilon noticed Chi's current condition. Upsilon's face contorted into a look of horror, and all Michiko did was turn away sadly._

"His heart will surely turn to ice."

…

Focusing back on reality, he lashed out at any scientist who dared come near him. Many had escaped, but the few who couldn't leave or were too brave to flee were fatally wounded. One woman received a pen through her neck, a older man was decapitated then slashed to ribbons. Chi saw out of the corner of his eye Moe levitate his trainer off the ground, then both disappeared into the hallway.

" _You will not escape!"_ He hissed, and followed them through the doorway. He darted through the door just in time to see Dr. Kaoru being teleported away, and Upsilon and her trainer rushing to them from down the hallway. Chi forgot about Moe and his trainer, and barreled past Moe to quench the bloodlust he was feeling. He wanted _her_ to suffer like he did. He pulled a fist back, but Michiko launched a crackling orb of dark energy directly to his face before he could make contact. The last thing he saw before he fell unconscious was Michiko, with a hate filled glare, and an arm splayed out in front of a teary eyed Upsilon. His burning rage was replaced with a tired confusion as he fell onto a heap on the floor, but before his eyes shut, he saw something he contemplated whether it was real or not.

A shimmery pink kitten was floating behind Upsilon, shaking its head and gazing down at him with a mournful gaze.

" _Control your temper,"_ A gentle voice spread through his mind, it was soothing, but stern. " _If you cannot restrain yourself, then your life will be over before I can free you."_

His final thoughts were of the possibility of freedom the strange voice promised.


End file.
